The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

The neural mechanisms underlying genetic risk for schizophrenia, a highly heritable psychiatric condition, are still under investigation. New schizophrenia risk genes discovered through genome-wide association studies (GWAS), such as neurogranin (NRGN), can be used to identify these mechanisms. In this study we examined the association of two common NRGN risk single nucleotide polymorphisms (SNPs) with functional and structural brain-based intermediate phenotypes for schizophrenia. We obtained structural, functional MRI and genotype data of 92 schizophrenia patients and 114 healthy volunteers from the multisite Mind Clinical Imaging Consortium study. Two schizophrenia-associated NRGN SNPs (rs12807809 and rs12541) were tested for association with working memory-elicited dorsolateral prefrontal cortex (DLPFC) activity and surface-wide cortical thickness. NRGN rs12541 risk allele homozygotes (TT) displayed increased working memory-related activity in several brain regions, including the left DLPFC, left insula, left somatosensory cortex and the cingulate cortex, when compared to non-risk allele carriers. NRGN rs12807809 non-risk allele (C) carriers showed reduced cortical gray matter thickness compared to risk allele homozygotes (TT) in an area comprising the right pericalcarine gyrus, the right cuneus, and the right lingual gyrus. Our study highlights the effects of schizophrenia risk variants in the NRGN gene on functional and structural brain-based intermediate phenotypes for schizophrenia. These results support recent GWAS findings and further implicate NRGN in the pathophysiology of schizophrenia by suggesting that genetic NRGN risk variants contribute to subtle changes in neural functioning and anatomy that can be quantified with neuroimaging methods.

Tesis por compendio / [ES] Un objetivo fundamental en los programas de conservación es mantener la diversidad genética y la estrategia de gestión más eficiente para lograrlo es aplicar el método de Contribuciones Óptimas. Este método optimiza las contribuciones de los candidatos a reproductores minimizando el parentesco global ponderada, lo que conduce a niveles más altos de diversidad genética, medida como heterocigosis esperada, y a un control efectivo del aumento de consanguinidad. El parámetro fundamental de este método es la matriz de parentesco. Esta matriz se ha obtenido tradicionalmente a partir del pedigrí, pero la disponibilidad actual de genotipos para un gran número de polimorfismos de un solo nucleótido (SNP) nos permite estimarla con una mayor precisión. Sin embargo, se han propuesto muchas medidas de parentesco genómico y se desconoce qué medida es la más apropiada para minimizar la pérdida de diversidad genética. Por lo tanto, el objetivo general de esta tesis fue investigar la eficiencia de diferentes matrices genómicas de parentesco en la gestión de poblaciones en programas de conservación, cuando se aplica el método de Contribuciones Óptimas. Las matrices comparadas fueron aquellas basadas en: i) la proporción de alelos compartidos por dos individuos (CSIM); ii) las desviaciones del número observado de alelos compartidos por dos individuos respecto del número esperado (CL&H); iii) la matriz de relaciones genómicas obtenida a través el método 1 de VanRaden (CVR1); iv) la matriz de relaciones genómicas obtenida a través el método 2 de VanRaden (CVR2); v) la matriz de relaciones genómicas obtenida a través el método de Yang (CYAN); y vi) segmentos idénticos por descendencia (CSEG). Los resultados para una sola generación, usando miles de SNP genotipados en individuos de una población cultivada de rodaballo, mostraron grandes diferencias en la magnitud de los seis coeficientes de parentesco. Las correlaciones entre los diferentes coeficientes variaron mucho, siendo las más bajas aquellas entre CSIM, CL&H o CSEG y CVR2 o CYAN. La gestión que utiliza matrices basadas en la proporción de alelos o segmentos compartidos (CSIM, CL&H y CSEG) retuvieron una mayor diversidad que aquella que utiliza matrices de relaciones genómicas (CVR1, CVR2 y CYAN). Como era de esperar, maximizar la heterocigosis llevó los alelos hacia frecuencias intermedias. Sin embargo, alejar las frecuencias alélicas de las frecuencias iniciales puede ser indeseable, ya que se pueden perder adaptaciones particulares al medio. Se utilizaron simulaciones estocásticas para investigar la eficiencia de CL&H y CVR2 en el manejo de poblaciones no divididas a lo largo de 50 generaciones y ambas matrices se compararon tanto en términos de la diversidad genética como en términos de los cambios asociados en las frecuencias alélicas. EL uso de CL&H en el método de Contribuciones Óptimas llevó a una mayor diversidad genética pero también en un mayor cambio de frecuencias alélicas que el uso de CVR2. Las diferencias entre estrategias fueron menores cuando sólo se usaron SNP con una frecuencia del alelo menos común (MAF) por encima de un umbral particular (MAF > 0.05 y MAF > 0.25) para calcular CL&H y CVR2 así como cuando se aplicó el método de Contribuciones Óptimas en poblaciones con censo más pequeños (se pasó de N = 100 a N = 20). La evaluación de CL&H y CVR2 se extendió a poblaciones subdivididas, también a través de simulaciones por ordenador. En poblaciones subdivididas, la diversidad genética se distribuye en dos componentes: dentro y entre subpoblaciones. Cuando se otorga un mayor peso al componente dentro de subpoblaciones, es posible restringir los niveles de consanguinidad. Bajo este escenario, la utilización de CL&H resultó ser la mejor opción para gestionar este tipo de poblaciones, ya que mantuvo una mayor diversidad global, condujo a una menor consanguinidad y a cambios en las frecuencias similares a los observados cuando se utilizó CVR2. / [CA] Un objectiu fonamental en els programes de conservació és mantindré la diversitat genètica i l'estratègia de gestió més eficient per aconseguir-ho és aplicar el mètode de contribucions òptimes. Aquest mètode optimitza les contribucions dels candidats a reproductors minimitzant el parentiu global ponderat, cosa que condueix a nivells més alts de diversitat genètica, mesurada com a heterozigosi esperada, i a un control efectiu de l'augment de consanguinitat. El paràmetre fonamental d'aquest mètode és la matriu de parentiu. Aquesta matriu s'ha obtingut tradicionalment a partir del pedigrí, però la disponibilitat actual de genotips per a un gran nombre de polimorfismes d'un sol nucleòtid (SNP) ens permet estimar-la amb més precisió. Tot i això, s'han proposat moltes mesures de parentiu genòmic i es desconeix quina mesura és la més apropiada per minimitzar la pèrdua de diversitat genètica. Per tant, l'objectiu general d'aquesta tesi va ser investigar l'eficiència de diferents matrius genòmiques de parentiu en la gestió de poblacions en programes de conservació, quan s'aplica el mètode de Contribucions Òptimes. Les matrius comparades van ser aquelles basades en: i) la proporció d'al·lels compartits per dos individus (CSIM); ii) les desviacions del nombre observat d'al·lels compartits per dos individus respecte del nombre esperat (CL&H); iii) la matriu de relacions genòmiques obtinguda a través del mètode 1 de VanRaden (CVR1); iv) la matriu de relacions genòmiques obtinguda a través del mètode 2 de VanRaden (CVR2); v) la matriu de relacions genòmiques obtinguda a través del mètode de Yang (CYAN); i vi) segments idèntics per descendència (CSEG). Els resultats per a una sola generació, usant milers d'SNP genotipats en individus d'una població cultivada de turbot, van mostrar grans diferències en la magnitud dels sis coeficients de parentiu. Les correlacions entre els coeficients van variar molt, sent les més baixes aquelles entre CSIM, CL&H o CSEG i CVR2 o CYAN. La gestió que utilitza matrius basades en la proporció d'al·lels o segments compartits (CSIM, CL&H i CSEG) van retindré una diversitat més gran que aquella que utilitza matrius de relacions genòmiques (CVR1, CVR2 i CYAN). Com calia esperar, la màxima heterozigosi va portar els al·lels cap a freqüències intermèdies. No obstant això, allunyar les freqüències al·lèliques de les freqüències inicials pot ser indesitjable, ja que es poden perdre adaptacions particulars al medi. Es van fer servir simulacions estocàstiques per investigar l'eficiència de CL&H i CVR2 en el maneig de poblacions no dividides al llarg de 50 generacions i les dues matrius es van comparar tant en termes de la diversitat genètica com en termes dels canvis associats a les freqüències al·lèliques. L'ús de CL&H en el mètode de Contribucions Òptimes va resultar en una major diversitat genètica però també en un canvi més gran de freqüències al·lèliques que l'ús de CVR2. Les diferències entre estratègies van ser menors quan només es van fer servir SNP amb una freqüència de l'al·lel menys comú (MAF) per sobre d'un llindar particular (MAF > 0.05 i MAF > 0.25) per calcular CL&H i CVR2 així com quan es va aplicar el mètode de Contribucions Òptimes en poblacions amb cens més petit (es va passar de N = 100 a N = 20). L'avaluació de CL&H i CVR2 es va estendre a poblacions subdividides, també a través de simulacions per ordinador. En poblacions subdividides, la diversitat genètica es distribueix en dos components: dins i entre subpoblacions. Quan s'atorga un pes més gran al component dins de subpoblacions, és possible restringir els nivells de consanguinitat. Sota aquest escenari, la utilització de CL&H va resultar ser la millor opció per gestionar aquest tipus de poblacions, ja que va mantindré una diversitat global més gran, va conduir a una menor consanguinitat i a canvis en les freqüències similars als observats quan es va utilitzar CVR2. / [EN] A main objective in conservation programs is to maintain genetic diversity, and the most efficient management strategy to achieve it is to apply the Optimal Contributions method. This method optimizes the contributions of breeding candidates by minimizing the global weighted coancestry. This leads to the highest levels of genetic diversity, when measured as expected heterozygosity, and to an effective control of the increase of inbreeding. The fundamental parameter of the method is the coancestry matrix which, traditionally, has been obtained from pedigree data. The current availability of genome-wide information allows us to estimate coancestries with higher precision. However, many different genomic coancestry measures have been proposed and it is unknown which measure is more efficient to minimize the loss of genetic diversity. Thus, the general aim of this thesis was to investigate the efficiency of different genomic coancestry matrices in the management of conserved populations when the Optimal Contributions method is applied to maximize genetic diversity. The matrices compared were those based on: i) the proportion of shared alleles (CSIM); ii) deviations of the observed number of alleles shared by two individuals from the expected number (CL&H); iii) the realized relationship matrix obtained by VanRaden's method 1 (CVR1); iv) the realized relationship matrix obtained by VanRaden's method 2 (CVR2); v) the realized relationship matrix obtained by Yang¿s method (CYAN); and vi) identical by descent segments (CSEG). Results for a single generation using thousands of SNP genotyped in individuals from a farm turbot population, showed large differences in the magnitude of the six coancestry coefficients. Moreover, pairwise correlations were those between coefficients greatly varied (especially for self-coancestry). The lowest correlations between CSIM, CL&H or CSEG and CVR2 or CYAN. Management with matrices based on the proportion of shared alleles or on segments (CSIM, CL&H and CSEG) retained higher variability than those based on realized genomic relationship matrices (CVR1, CVR2 and CYAN). As expected, maximizing heterozygosity pushed alleles toward intermediate frequencies. However, moving allele frequencies away from initial frequencies may be undesirable as particular adaptations to the environment can be lost. Stochastic simulations were used to investigate the efficiency of CL&H and CVR2 in the management of an undivided population across 50 generations and both matrices were compared not only in terms of the genetic diversity maintained but also in terms of the associated changes in allele frequencies across generations. The use of CL&H in the Optimal Contribution method resulted in a higher genetic diversity but also in a higher change of allele frequencies than the use of CVR2. The differences between strategies were reduced when only SNPs with a minimum allele frequency (MAF) above a particular threshold (MAF > 0.05 and MAF > 0.25) were used to compute CL&H and CVR2 as well as when the Optimal Contributions method was applied in populations of smaller sizes (N = 20 vs N = 100). The evaluation of CL&H and CVR2 was extended to subdivided populations, also via computer simulations. When populations are subdivided into different breeding groups, it is possible to give different weights to the within- and between-subpopulation components of genetic diversity. When a higher weight is given to the within-subpopulation component, the levels of inbreeding can be restricted. In this scenario, the use of CL&H was the best option for managing subdivided populations as it maintained more global diversity, led to less inbreeding and to changes in frequencies similar to those observed when using CVR2 when a large weight was given to the within-subpopulation term. / Esta tesis doctoral se realizó en el Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) de Madrid. El trabajo expuesto en el capítulo 2 se realizó en parte en el Instituto Roslin, de la Universidad de Edimburgo durante una estancia predoctoral. Los trabajos expuestos en la tesis han sido financiados con una beca predoctoral FPI (BES-2017-081070) y a través de proyectos del Plan Estatal de I+D+i del Ministerio de Ciencia e Innovación (proyectos CGL2016-75904-C2-2-P y PID2020- 114426GB-C22) y de la Unión Europea (‘European Union‘s Seventh Framework Program, KBBE.2013.1.2-10, under Grant Agreement No. 613611, FISHBOOST project’ y ‘European Commission Horizon 2020, Framework Programme through Grant Agreement No. 727315, MedAID project’). / Morales González, E. (2023). Management of Genetic Diversity in Conservation Programs Using Genomic Coancestry [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/195231 / Compendio

Die 3D Struktur von Chromosomen im Zellkern reguliert verschiedene Funktionen in der Zelle und Fehler in der 3D Faltung des Genoms können pathogen sein. 3D Genomfaltung kann mit verschiedenen Methoden untersucht werden um Chromatinkontakte, sowie die Position von DNA in Relation zu sub-nuklearen Bereichen oder der Kernmembran zu detektieren. Hier verwende ich GAM und Hi-C um zwei Aspekte der 3D Genomtopologie zu untersuchen, die Allelspezifität von Chromatinkontakten und Kontakte zwischen Chromosomen. Ich untersuche allelspezifische Kontakte in murinen embryonalen Stammzellen und Interaktionen zwischen Chromosomen im Zusammenhang mit Autismus Spektrum Störung auf ihre Relevanz in der Regulation von Genen. Zur allelspezifischen Detektion von Chromatinkontakten generierte ich einen GAM Datensatz der tausende von nuklearen Cryodünnschnitten enthält. Die Generierung dieser Daten beinhaltete die Entwicklung einer verbesserten Version der GAM Methode zur Produktion von großen Datensätzen in Hochdurchsatz. Hier zeige ich, dass GAM effizient Haplotyp-spezifische Chromatinkontakte bestimmen kann. Erste Untersuchungen von allelspezifischer 3D Genomtopologie zeigten weitreichende Unterschiede zwischen den Allelen, welche „A/B compartments“ und spezifische Chromatinkontakte beinhalten, wie zum Beispiel am Imprinting Locus H19/Igf2. Zur Untersuchung von interchromosomalen Kontakten detektierte ich Chromatinkontakte mit Hi-C im Kontext einer genomischen Deletion am humanen 16p11.2 Locus, assoziiert mit Autismus Spektrum Störung. Ich zeige hier, dass die Deletion am 16p11.2 Locus zu der Reorganisation von spezifischen interchromosomalen Kontakten zwischen 16p11.2 und Chromosom 18 führt, und stelle eine Hypothese auf wie diese interchromosomalen Kontakte zur ektopischen Aktivierung von Pcdh Genen auf Chromosom 18 führen. Protocadherins haben wichtige Funktionen in neuronaler Konnektivität, ein Prozess dessen Störung zur Manifestierung von Autismus Spektrum Störung beitragen könnte. / The 3D folding of interphase chromosomes inside the nucleus regulates important nuclear functions and once disrupted can lead to the manifestation of disease. Different techniques can be used to map 3D genome folding and detect pairwise and multiway interactions of the genome, or map the positions of DNA with respect to subnuclear compartments or the nuclear lamina. Here, I use GAM and Hi-C to explore two aspects of 3D genome topology, the allele specificity of chromatin contacts and long-range contacts between chromosomes, respectively. I detect specific contacts of the parental alleles in mouse embryonic stem cells and interactions between chromosomes in the context of congenital disease and study them with regard to their functionality and importance in mammalian gene regulation. For detecting chromatin contacts with allele specificity, I produced a GAM dataset containing thousands of nuclear slices. The collection of this data was accompanied by the development of a high-throughput version of GAM that allows the generation of large datasets. I show that GAM can determine haplotype-specific chromatin contacts with high efficiencies. First explorations of allele-specific chromatin topologies reveal many differences between the parental alleles, including allele-specific compartments A and B, and specific chromatin contacts, for example at the imprinted H19/Igf2 locus. For the exploration of inter-chromosomal contacts in disease, I mapped chromatin interactions with Hi-C in the context of a CNV at the human 16p11.2 locus, associated with autism spectrum disorders. Here, I show that the deletion at the 16p11.2 locus results in the rearrangement of specific inter-chromosomal contacts between the 16p11.2 locus and chromosome 18 and propose a role for these inter-chromosomal contact changes in the upregulation of the nearby Pcdhb gene cluster, which comprises protocadherin genes with important functions in neuronal connectivity during development.

Aquest treball és una contribució als estudis de diversitat del genoma humà i pretén estudiar la variació genètica existent a nivell mundial en dos gens, causants de malaltia, el gen CFTR i el gen GBA, en cromosomes d'individus sans. Mutacions en aquests gens produeixen la fibrosi quística i la malaltia de Gaucher respectivament. La fibrosi quística és la malaltia autosòmica recessiva més comuna en poblacions europees. La malaltia de Gaucher és la malaltia lisosòmica d'acumulació lipídica més freqüent. L'estudi analitza la variació genètica en diferents polimorfismes d'ambdós gens; reconstrueix els haplotips i analitza la seva distribució geogràfica; i analitza l'extensió i distribució geogràfica del desequilibri de lligament entre loci. Pel gen GBA, hem ampliat la regió, abastant fins al gen PKLR (que codifica per a la piruvat quinasa). A més a més, pel cas de CFTR, pot ajudar a entendre l'origen de les mutacions més freqüents causants de fibrosi quística. / This work is a contribution to human genome diversity studies and it aims to study the world-wide genetic variation that exists in two disease genes, CFTR and GBA gene, in healthy chromosomes. Mutations in these genes are known to cause cystic fibrosis and Gaucher disease respectively. Cystic fibrosis is the most common severe autosomal recessive disease in patients of European descent. Gaucher disease is the most frequent lysosomal storage disorder. The study analyzes the genetic variation in CFTR and GBA polymorphisms; estimates haplotype frequencies and describes their geographic distribution; and measures linkage disequilibrium between loci. For GBA gene, we have extended the analysis covering PKLR gene (that encodes for a pyruvate kinase). Moreover, for CFTR gene, we have tried to understand the origin of the most common cystic fibrosis causing mutations.

Tortilla sales are projected to exceed 9.5 billion by 2014. However, currently no wheat cultivars have been identified that possess the intrinsic quality attributes needed for the production of optimum quality tortillas. Tortillas made with refined wheat flour low in dietary fiber (DF) are popular in the United States due to their sensory properties. This study explored the use of wheat lines (WL) possessing variations in high molecular weight glutenin allele sub-units (HMW-GS) for production of tortillas and also investigated the use of corn based resistant starches (RS), type II (RS2) and wheat based RS type IV (RS4) to increase DF in tortillas. Tortillas were made with 0-15 percent RS and 100 percent whole white wheat (WW). Flour protein profiles, dough, and tortilla properties were evaluated to determine the effects of the allelic variations and RS substitution on tortilla quality. Sensory properties of tortillas with RS were determined. Variations in HMW-GS composition significantly affected the protein quality and tortilla properties. Flour from WL possessing allelic combinations (2*, 17+18, 7, 2+12), (1, 17+18, 5+10), (2*, 17, 2+12) and (1, 2*, 17+18, 2+12) had 12.8-13.3 percent protein. These WL had extensible doughs and produced large diameter tortillas with superior (greater than or equal to 3.0) flexibility after 16 days compared to control. However, WL with (17+18 and 5+10) and (2*, 17+7, 5) produced extensible doughs, large, but less flexible, tortillas compared to control. WL with (2*,17+18,5+10) and (1,2*,7+9,5+10) produced smaller diameter tortillas, but with superior flexibility compared to control. RS2, WW, and cross-linked-pre-gelatinized RS4 (FiberRite) produced hard, less-extensible doughs and thinner tortillas compared to control, due to high water absorption. Cross-linked RS4 (Fibersym) dough and tortillas were comparable to control. 15 percent of RS2 and RS4 increase DF in control to 6 and 14 percent respectively, compare to control (2.8 percent DF). WW tortillas were less acceptable than control in appearance, flavor and texture, while tortillas with 15 percent Fibersym had higher overall acceptability than control. RS2 negatively affected dough machinability and tortilla shelf stability. However, 15 percent RS4 improved the DF in refined flour tortillas to meet FDA's "good source of fiber claim," without negatively affecting dough/tortilla quality.

No description available.

L'épigénome est défini par l’ensemble de l’information chromatinienne autre que celle fournie par la séquence ADN. Au sein d'une même espèce et pour un type cellulaire donné, chaque individu présente des caractéristiques particulières de l'épigénome. Les épi-polymorphismes, définis comme étant les différences inter-individus de marques chromatiniennes, sont encore partiellement caractérisés et peuvent être liés aux phénotypes de chacun. La première partie de mon travail a été d'identifier et d'interpréter chez S.cerevisiae l'impact des épi-polymorphismes de modification des queues d'histones. Pour y parvenir, j'ai cartographié les épigénomes de cinq modifications différentes (3 acétylations et 2 méthylations) chez trois souches de levures issues de différents isolats naturels. Par une méthode de ChIP-seq et le développement d'un outil informatique, j'ai comparé les épigénomes de ces souches à l'échelle de nucléosomes individuels. L'étude des propriétés génomiques des épi-polymorphismes m'a alors permis de découvrir certaines caractéristiques encore inconnues et décrites dans ce manuscrit.Par ailleurs, j'ai voulu aborder le lien entre épi-polymorphismes et réponse transcriptionnelle à l'environnement. Pour cela, j'ai construit un jeu de souches mutantes dérivées de souches naturelles, où certains épi-polymorphismes ne peuvent plus être maintenus. J'ai analysé par RNA-seq les transcriptomes de certaines de ces souches avant et après un changement environnemental. Malheureusement, l'analyse des résultats a révélé que la qualité des données ne permettent pas d'établir le lien recherché mais les outils mis en place sont désormais disponibles.J'ai enfin étudié la dynamique d'évolution d'un épigénome en présence ou en l'absence de pression de sélection. Pour cela, j'ai suivi une modification d'histone (l'acétylation de la lysine 14 de l'histone H3) chez la levure pendant 1.000 générations dans deux conditions d'évolution expérimentale différentes : l'une sélective, l'autre neutre. J'ai mis en évidence des différences remarquables et inattendues entre ces deux régimes évolutifs. Des études mécanistiques détaillées restent à faire pour caractériser la nature et les propriétés de ces différences. / Epigenome is defined as the entire chromatin information other than the DNA sequence. Within a given species and for a given cell type, each indivual has specific epigenomic characteristics. Epigenomic differences between individuals (refered to as 'epi-polymorphisms') remain poorly characterized, although cases were reported where they could be linked to phenotypic differences. In my thesis, I used the model organism S. cerevisiae to identify histone modification epi-polymorphisms and study their biological impact. I profiled the epigenome of five different histone modifications (3 acetylations and 2 methylations) in three natural yeast strains. By ChIP-seq methods and software developments, I compared these strains at single-nucleosome resolution and discovered novel characteristics of these epi-polymorphisms which are described in this manuscript.Furthermore, I constructed a research framework to investigate the link between epi-polimorphisms and response to environmental cues. For this, I built a set of mutant strains derived from natural strains but where some epi-polymorphisms can no longer be maintained. I analyzed by RNA-seq the transcriptomes of some of these mutant strains before and after an environmental shift. Unfortunately, the quality of this initial data produced was not sufficient to link epi-polymorphisms to differntial responses, but the strain resources remain available for further investigations. Finally, I studied the evolutionary dynamics of epi-polymorphisms in the presence or absence of selection pressure. To do so, I followed the evolution of H3K14ac for 1.000 generations under two conditions of yeast experimental evolution ( selective or neutral). Marked differences were observed between the two regimes, revealing unexpected consequences of the presence of selection. Further mechanistic studies will be needed to elucidate the full properties of these differences.

No description available.

Genome-wide association studies have greatly improved our understanding of the contribution of common variants to the genetic architecture of complex traits. However, two major limitations have been highlighted. First, common variant associations typically do not identify the causal variant and/or the gene that it is exerting its effect on to influence a trait. Second, common variant associations usually consist of variants with small effects. As a consequence, it is more challenging to harness their translational impact. Association studies of rare variants and complex traits may be able to help address these limitations. Empirical population genetic data shows that deleterious variants are rare. More specifically, there is a very strong depletion of common protein truncating variants (PTVs, commonly referred to as loss-of-function variants) in the genome, a group of variants that have been shown to have large effect on gene function, are enriched for severe disease-causing mutations, but in other instances may actually be protective against disease. This thesis is divided into three parts dedicated to the study of protein truncating variants, their medical relevance, and their functional consequences. First, I present statistical, bioinformatic, and computational methods developed for the study of protein truncating variants and their association to complex traits, and their functional consequences. Second, I present application of the methods to a number of case-control and quantitative trait studies discovering new variants and genes associated to breast and ovarian cancer, type 1 diabetes, lipids, and metabolic traits measured with NMR spectroscopy. Third, I present work on improving annotation of protein truncating variants by studying their functional consequences. Taken together, these results highlight the utility of interrogating protein truncating variants in medical and functional genomic studies.